James Hird wants ASADA's long-running investigation into the Essendon supplements scandal to start all over again, this time without the AFL.

The Bombers coach will return to the Federal Court on Monday to appeal against September's devastating verdict.

His lawyers are challenging the finding by Justice John Middleton that ASADA acted lawfully by conducting a joint investigation with the AFL into Essendon's 2011-12 supplements program.

Hird and ASADA have lodged documents with the Federal Court, making detailed submissions about their arguments ahead of the appeal.

The Hird camp claims Justice Middleton erred in several areas, while ASADA calls the appeal misconceived.

If Hird succeeds, he expects ASADA's investigation to start again from scratch.

"The investigation must ... start over and be carried out according to law," Hird's lawyers said.

"The analogy is with a court declaring a search warrant invalid and requiring the investigating authority to act lawfully if it wishes to re-issue the warrant.

"(ASADA) must start again and investigate according to law.

"Further, there is no basis for suggesting that the AFL and the interviewees would respond in the same way today - there would be no joint investigation."

In the wake of Justice Middleton's findings, ASADA issued amended show cause notices to 34 current and past Essendon players.

Hird and Essendon made a joint legal challenge against the ASADA investigation and were stunned when Justice Middleton ruled decisively in favour of the anti-doping body.

The coach then broke ranks with the club by deciding to appeal.

Hird's decision prompted strong speculation at the start of last month that the Bombers might sack him.

But the Bombers then confirmed he would stay coach and Hird is adamant he will be in charge at Essendon next season.

Hird's submission makes several arguments against the original verdict.

"The judge failed to establish any statutory basis ASADA ... to enter into, and implement, an agreement with the AFL to investigate anti-doping violations under the Australian Sports Anti-Doping Authority Act ... or to institute and conduct ASADA's investigation in concert with the AFL, as they did," they argue in their court documents.

Similarly, ASADA have lodged a detailed argument against the appeal.

Lawyers for ASADA also argue that the show-cause notices should be allowed to proceed.

"If the interests of the 34 players are relevant, so too are the interests of the AFL and the public at large," the lawyers said.

"Those interests militate strongly against permanent injunctive relief and favour non-interference with the show cause notices - particularly since they have re-issued.

"The evidence since judgment is that, apart from the appellant, all (or nearly all) stakeholders favour a full and expeditious consideration of possible ADRVs (anti-doping rule violations) 'on the merits'."